Short open reading frames (sORFs) are codon sequences with a start and stop codon within atmost 100 codons. Cells produce many transcripts from them and some sORFs have been found to have function. sORFs have been associated with embryogenesis, myogenesis, immunity and various diseases including cancers. Cell culture screening is a common method to study function in sORFs. By inserting mutations in known sORF locations one can affect their translation by removing start codons, inserting premature stop codons, or removing native stop codons. A new tool set to do this isCRISPR technology, where single guide RNA (gRNA) can be used to make more precise genome edits. Unfortunately, such design is nontrivial and suggests a lot of variants for testing. It results in a back-and-forth testing process involving different available design tools. In this project, a comprehensive way was developed to see and iterate over the many test combinations. This intends to ease the process and decrease the likelihood for errors. The developed solution is a tool that integrates the currently best design tools. It also introduces a method in the form of a new quality summary score that can evaluate the estimated outcomes of the various designed guide variants. The tool was tested, and it was found that the score simplifies and amplifies the earlier usedscore methods. The pipeline is simple to install and use, integrates the currently most actively developed tools, and an installation is as future proof as can be made in a rapidly evolving field.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-511855 |
| Date | January 2023 |
| Creators | Torbjörn, Larsson |
| Publisher | Uppsala universitet, Institutionen för biologisk grundutbildning |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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